Commit 88894538 authored by Holger Brandl's avatar Holger Brandl

fixed cs_lib_size

parent 95672d3d
......@@ -104,7 +104,7 @@ export -f cs_bowtie_qc
cs_lib_size(){
rm -f algn_counts.txt
for bamFile in $(ls $*); do
for bamFile in $(ls *.bam); do
(
echo "processing $bamFile"
samtools flagstat $bamFile | head -n1 | cut -f1 -d' ' | sed -e 's/$/\t'$(basename $bamFile .bam)'/' >> algn_counts.txt
......@@ -119,7 +119,8 @@ devtools::source_url("https://raw.githubusercontent.com/holgerbrandl/datautils/v
libSizes <- read_tsv("algn_counts.txt", col_names=F) %>% set_names(c("library_size", "sample"))
libSizes %>% ggplot(aes(sample, library_size)) +
geom_bar(stat="identity") +
ggtitle("algn_counts") +
scale_y_continuous(labels=comma) +
ggtitle("# alignments") +
coord_flip()
ggsave2()
......
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